RS6 - BACSU - GREMLIN Contacts

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RS6 - 30S ribosomal protein S6

UniProt:	P21468	Sequences: MRKYEVMYIIRPNIDEESKKAVIERFNNVLTSNGAEITGTKDWGKRRLAYEINDFRDGFYQIVNVQSDAAAVQEFDRLAKISDDIIRHIVVKEEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	95 (94)
Sequences:	2193 (1230)
Seq/√Len:	126.9

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_L	35_A	3.827	1.00
28_N	32_S	3.401	1.00
9_I	58_G	3.391	1.00
36_E	66_Q	3.311	1.00
7_M	62_I	2.337	1.00
38_T	66_Q	2.081	1.00
51_E	56_R	2.042	1.00
20_K	42_D	1.991	1.00
27_N	31_T	1.977	1.00
13_N	55_F	1.896	1.00
24_E	28_N	1.883	1.00
74_E	77_R	1.834	1.00
12_P	55_F	1.784	1.00
76_D	88_H	1.779	1.00
3_K	66_Q	1.773	1.00
11_R	55_F	1.724	1.00
15_D	18_S	1.674	1.00
6_V	65_V	1.635	1.00
27_N	40_T	1.615	1.00
45_K	57_D	1.608	1.00
10_I	22_V	1.578	1.00
6_V	79_A	1.546	1.00
47_R	57_D	1.517	1.00
28_N	31_T	1.510	1.00
24_E	27_N	1.499	1.00
52_I	87_R	1.499	1.00
76_D	90_V	1.485	1.00
10_I	14_I	1.483	1.00
39_G	64_N	1.438	1.00
2_R	92_K	1.420	1.00
55_F	86_I	1.409	1.00
75_F	79_A	1.394	1.00
33_N	71_A	1.344	1.00
6_V	75_F	1.301	1.00
42_D	59_F	1.271	1.00
68_D	71_A	1.214	0.99
8_Y	63_V	1.212	0.99
20_K	24_E	1.204	0.99
67_S	72_V	1.190	0.99
48_L	86_I	1.123	0.99
69_A	73_Q	1.095	0.99
22_V	84_D	1.086	0.99
40_T	63_V	1.062	0.99
31_T	36_E	1.052	0.98
29_V	33_N	1.031	0.98
30_L	71_A	1.015	0.98
77_R	81_I	1.007	0.98
8_Y	61_Q	0.999	0.98
76_D	80_K	0.988	0.98
72_V	90_V	0.971	0.97
6_V	90_V	0.922	0.96
70_A	73_Q	0.890	0.96
16_E	20_K	0.889	0.96
11_R	84_D	0.886	0.95
64_N	93_E	0.883	0.95
10_I	85_I	0.869	0.95
19_K	59_F	0.866	0.95
79_A	85_I	0.859	0.95
21_A	24_E	0.857	0.95
74_E	78_L	0.852	0.94
46_R	60_Y	0.835	0.94
42_D	61_Q	0.825	0.93
25_R	82_S	0.806	0.93
47_R	59_F	0.802	0.92
7_M	91_V	0.799	0.92
27_N	63_V	0.798	0.92
26_F	79_A	0.797	0.92
73_Q	76_D	0.783	0.92
46_R	87_R	0.778	0.91
43_W	62_I	0.776	0.91
26_F	75_F	0.771	0.91
29_V	77_R	0.763	0.90
29_V	78_L	0.760	0.90
26_F	47_R	0.750	0.90
8_Y	27_N	0.737	0.89
33_N	68_D	0.737	0.89
31_T	37_I	0.735	0.89
29_V	71_A	0.730	0.88
26_F	82_S	0.729	0.88
23_I	61_Q	0.725	0.88
9_I	86_I	0.722	0.88
10_I	58_G	0.721	0.88
67_S	71_A	0.710	0.87
65_V	79_A	0.694	0.86
19_K	42_D	0.682	0.85
78_L	82_S	0.678	0.84
80_K	88_H	0.670	0.84
25_R	83_D	0.648	0.82
24_E	40_T	0.647	0.82
35_A	71_A	0.641	0.81
29_V	74_E	0.637	0.81
18_S	21_A	0.636	0.80
7_M	89_I	0.635	0.80
78_L	94_E	0.633	0.80
47_R	56_R	0.631	0.80
71_A	75_F	0.625	0.79
78_L	81_I	0.611	0.78
19_K	45_K	0.611	0.78
26_F	78_L	0.610	0.78
13_N	46_R	0.610	0.78
10_I	23_I	0.606	0.77
38_T	64_N	0.602	0.77
8_Y	58_G	0.600	0.77
22_V	26_F	0.599	0.76
27_N	89_I	0.596	0.76
14_I	22_V	0.590	0.75
16_E	19_K	0.590	0.75
16_E	59_F	0.586	0.75
53_N	86_I	0.586	0.75
2_R	69_A	0.585	0.75
69_A	72_V	0.584	0.75
40_T	61_Q	0.577	0.74
74_E	91_V	0.571	0.73
8_Y	23_I	0.560	0.72
17_E	21_A	0.558	0.71
65_V	90_V	0.548	0.70
7_M	43_W	0.544	0.69
16_E	45_K	0.539	0.69
11_R	56_R	0.534	0.68
7_M	93_E	0.533	0.68
30_L	75_F	0.532	0.68
6_V	63_V	0.527	0.67
45_K	59_F	0.526	0.67
6_V	81_I	0.525	0.67
25_R	47_R	0.522	0.66
7_M	44_G	0.521	0.66
64_N	85_I	0.519	0.66
51_E	54_D	0.515	0.65
43_W	46_R	0.514	0.65
23_I	27_N	0.513	0.65
18_S	22_V	0.510	0.64
12_P	16_E	0.506	0.64
27_N	61_Q	0.504	0.64
22_V	25_R	0.503	0.63
88_H	91_V	0.503	0.63
37_I	63_V	0.503	0.63
46_R	79_A	0.502	0.63
69_A	76_D	0.502	0.63
79_A	88_H	0.502	0.63
34_G	56_R	0.502	0.63
14_I	19_K	0.500	0.63

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
1vmbA	1	1	100	0.1	Contact Map
1cqmA	1	1	100	0.104	Contact Map
3r3tA	3	0.9895	100	0.106	Contact Map
2j5aA	1	1	100	0.11	Contact Map
3bbnF	1	1	100	0.112	Contact Map
4kiyF	1	0.9895	100	0.116	Contact Map
4tp8F	1	0.9895	100	0.12	Contact Map
5aj3F	1	0.9789	100	0.167	Contact Map
2kjwA	1	0.5684	99.8	0.434	Contact Map
3zzpA	1	0.4105	99.1	0.63	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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